Variant report

Variant	rs12825843
Chromosome Location	chr12:58352220-58352221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:58339593..58341366-chr12:58350590..58353556,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10506393	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10783860	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783864	0.83[ASN][1000 genomes]
rs10783865	0.82[EUR][1000 genomes]
rs10877048	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877050	0.81[ASN][1000 genomes]
rs10877052	0.83[EUR][1000 genomes]
rs11172408	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172418	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172419	0.81[ASN][1000 genomes]
rs11172420	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11172421	0.83[EUR][1000 genomes]
rs11172422	0.83[EUR][1000 genomes]
rs11608333	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11608939	0.81[ASN][1000 genomes]
rs12366757	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12366794	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12368024	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12422985	0.83[EUR][1000 genomes]
rs12828647	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1304496	0.81[ASN][1000 genomes]
rs1466972	0.81[ASN][1000 genomes]
rs1466973	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1605333	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17120134	0.81[ASN][1000 genomes]
rs1848129	0.87[ASN][1000 genomes]
rs2102349	0.81[ASN][1000 genomes]
rs2221541	0.83[EUR][1000 genomes]
rs2372377	0.81[ASN][1000 genomes]
rs2372378	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2372379	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2659659	0.82[ASN][1000 genomes]
rs2659662	0.84[ASN][1000 genomes]
rs2717404	0.81[ASN][1000 genomes]
rs2720191	0.81[ASN][1000 genomes]
rs2888299	0.81[ASN][1000 genomes]
rs3858557	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3858558	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3913866	0.81[ASN][1000 genomes]
rs3933982	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4495927	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4565944	0.81[EUR][1000 genomes]
rs4604932	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4760175	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760181	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760182	0.83[EUR][1000 genomes]
rs6581170	0.82[EUR][1000 genomes]
rs6581173	0.82[EUR][1000 genomes]
rs6581177	0.81[EUR][1000 genomes]
rs7132168	0.81[EUR][1000 genomes]
rs7132521	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7135063	0.82[EUR][1000 genomes]
rs7304458	0.83[EUR][1000 genomes]
rs7314066	0.81[EUR][1000 genomes]
rs7484670	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7954291	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7959747	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7960690	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7960942	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7963367	0.83[EUR][1000 genomes]
rs7974754	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7975805	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7977671	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs871908	0.82[EUR][1000 genomes]
rs951901	0.83[EUR][1000 genomes]
rs970249	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases
2	nsv523853	chr12:58350631-58386722	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv975500	chr12:58351052-58362673	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12825843	XRCC6BP1	cis	uninvolved skin	skin_eQTL
rs12825843	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs12825843	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs12825843	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs12825843	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs12825843	XRCC6BP1	cis	lung	GTEx
rs12825843	XRCC6BP1	cis	Artery Tibial	GTEx
rs12825843	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs12825843	XRCC6BP1	cis	multi-tissue	Pritchard
rs12825843	XRCC6BP1	cis	Whole Blood	GTEx
rs12825843	XRCC6BP1	cis	Thyroid	GTEx
rs12825843	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs12825843	XRCC6BP1	cis	Artery Aorta	GTEx
rs12825843	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs12825843	XRCC6BP1	cis	Nerve Tibial	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58336000-58353000	Weak transcription	Small Intestine	intestine
2	chr12:58336200-58353000	Weak transcription	Stomach Mucosa	stomach
3	chr12:58336200-58353400	Weak transcription	Fetal Kidney	kidney
4	chr12:58336200-58353600	Weak transcription	Brain Substantia Nigra	brain
5	chr12:58336200-58353600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:58336200-58353800	Weak transcription	Brain Angular Gyrus	brain
7	chr12:58336200-58353800	Weak transcription	Brain Hippocampus Middle	brain
8	chr12:58336200-58354000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:58336200-58354000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:58336200-58354000	Weak transcription	Psoas Muscle	Psoas
11	chr12:58336200-58356200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:58336200-58359600	Weak transcription	A549	lung
13	chr12:58336400-58359600	Weak transcription	HMEC	breast
14	chr12:58336800-58353000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:58337200-58358400	Weak transcription	HepG2	liver
16	chr12:58342800-58352400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:58343200-58352600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:58345000-58352600	Strong transcription	Dnd41	blood
19	chr12:58346400-58352600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:58347800-58352600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:58348200-58352400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr12:58348200-58352400	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:58348800-58353800	Weak transcription	Osteobl	bone
24	chr12:58350200-58352600	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:58350400-58352600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:58350400-58352600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:58350400-58352600	Strong transcription	Adipose Nuclei	Adipose
28	chr12:58350600-58352400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:58350600-58352800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:58350600-58355400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:58350800-58352600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:58351000-58352400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:58351000-58352400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:58351000-58352600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:58351000-58352600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:58351000-58352600	Strong transcription	Colonic Mucosa	Colon
37	chr12:58351000-58352600	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:58351200-58352400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:58351200-58352400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:58351200-58352400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
41	chr12:58351200-58352400	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr12:58351200-58352400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr12:58351200-58352400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:58351200-58352400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:58351200-58352400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:58351200-58352400	ZNF genes & repeats	Aorta	Aorta
47	chr12:58351200-58352400	ZNF genes & repeats	Esophagus	oesophagus
48	chr12:58351200-58352400	ZNF genes & repeats	Placenta	Placenta
49	chr12:58351200-58352400	Strong transcription	Left Ventricle	heart
50	chr12:58351200-58352400	ZNF genes & repeats	Lung	lung

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